Structural maintenance of Chromosome Hinge Domain Containing 1 (SMCHD1) regulates gene expression

Eukaryotic cells evolved by packaging genomic DNA into chromatin where DNA is wrapped around histones. This significantly reduces random transcriptional events by providing a barrier for gene expression. In addition, chemical modifications of histones and cytosine residues on DNA greatly impact regulation of gene expression. Structural maintenance of chromosome hinge domain containing 1 (SMCHD1) is a chromatin modifier. SMCHD1 was originally recognized as essential for X chromosome inactivation and survival in female mice where it plays a critical role in methylation of a subset of CpG islands. Structural studies suggest that SMCHD1 interaction with HP1 binding protein, HBiX1, mediates heterochromatin formation over the X chromosome by linking two chromatin domains enriched for repressive histone marks. In addition, loss of SMCHD1 is lethal in male mice in a mixed background, implying that SMCHD1 regulates genes on non-sex chromosomes. Thus, we identified a need to investigate the role of SMCHD1 in regulating expression of autosomal genes. In addition, I sought to determine SMCHD1 genome occupancy when global DNA methylation was greatly reduced and identify candidate binding partners. I used shRNA technology to knockdown SMCHD1 expression and identified genes that were up and down regulated in human embryonic kidney (HEK293) cells. A number of these genes are expressed in either a stochastic or parent-of-origin monoallelic fashion. Using chromatin immunoprecipitation-sequencing (ChIP), I identified genome-wide occupancy of SMCHD1 and showed that its genomic binding was sensitive to the DNA demethylating reagent, 5-azacytidine. SMCHD1 occupancy correlates with a number of genes belonging to the G protein-coupled receptor superfamily and loss of SMCHD1 in human neuroblastoma SH-SY5Y cells leads to increased levels of cellular cAMP. In addition, loss of SMCHD1 increases KCNQ1 expression, a subunit of the potassium voltage gated channel that plays a critical role in repolarization of the cardiac action potential. Moreover, using tandem tagged affinity purification, I investigated binding partners that potentially interact with SMCHD1 to regulate gene expression. Taken together, SMCHD1 might be involved in variety of diseases including Facioscapulohumeral Muscular Dystrophy (FSHD) and Bosma Arhinia Microphthalmia Syndrome (BAMS).